User: Rory Stark

gravatar for Rory Stark
Rory Stark1.7k
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Location:
CRUK, Cambridge, UK
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1 day, 16 hours ago
Joined:
4 years ago
Email:
r*********@cruk.cam.ac.uk

I am Principal Bioinformatics Analyst at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 283 results • page 1 of 29 • next >
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Answer: A: DiffBind: error with dba(sampleSheet="samples.csv")
... The peak files you are using are in bed format, with the score in the 5th column. In your sample sheet, you specified the format as "raw", which expects the score in the 4th column. So if you change the values in the last column of samples.csv from "raw" to "bed", it should work. -Rory ...
written 1 day ago by Rory Stark1.7k
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Comment: C: ChIPseq diffbind merging peaks
... Hi Veronique- No, I didn't get any email. rory.stark @ cruk.cam.ac.uk   ...
written 2 days ago by Rory Stark1.7k
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Comment: C: DiffBind MA plot
... The diagonals form when there is no signal in one sample group, but there are a concentration of overlapping reads in the other sample group. In that case there is a linear relationship between the mean concentration (mean number of reads in all samples) and fold change (essentially the mean number ...
written 2 days ago by Rory Stark1.7k
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Answer: A: DiffBind MA plot
... Hello Rob- Each dot in the plot represents a consensus binding site. For the X axis, "concentration" refers to the mean (normalized) number of reads across all the samples for that binding site. This is reported as a log2 value, so as you go from left to right, the overall binding affinity (read de ...
written 2 days ago by Rory Stark1.7k
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Answer: A: DiffBind: How to change the scatter plot colors?
... Hi Senthil- Currently there is not an official way to change the colors of the MA plots in DiffBind. I can think of two ways to get MA plots with different colors. One is to do your own plotting, and the other is to hack some un-exported variables. Suppose you want to change the color of the dots ...
written 6 days ago by Rory Stark1.7k
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Answer: A: ChIPseq diffbind merging peaks
... Hello Veronique- The peak calling step (in this case via MACS) can be imprecise, especially in “borderline” peaks. As you use a hard threshold, some regions may just miss being identified as peaks. You are correct that DiffBind re-counts overlapping reads for all consensus peaks in all samples. I ...
written 7 days ago by Rory Stark1.7k
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Comment: C: DiffBind BED output with score
... > report <- dba.report(tamoxifen, th=.05, DataType=DBA_DATA_FRAME) > scores <- -10*(log10(report$FDR)) > sites <- cbind(report[,1:3],rownames(report),scores) > gains <- report$Fold > 2 > losses <- report$Fold < -2 ​> write.table(site ...
written 14 days ago by Rory Stark1.7k
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Comment: C: DiffBind BED output with score
... This tool uses the score to rank sites. If you are using differentially bound sites from DiffBind, a score from DiffBind would be the best bet. For example: > data(tamoxifen_analysis) > report <- dba.report(tamoxifen, th=.05,   DataType=DBA_DATA_FRAME) > score < ...
written 14 days ago by Rory Stark1.7k
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Answer: A: Diffbind and dba.peakset vs dba.overlap
... The issue has to do with the minOverlap parameter to dba.peakset() (and other functions, such as dba.count). The key is that this parameter has a default value minOverlap=2. The vector returned by dba.overlap(...,mode=DBA_OLAP_RATE) contains the number of peaks that remain for different settings of ...
written 14 days ago by Rory Stark1.7k
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Answer: A: Diffbind analysis warning
... The data() command is used to load a dataset. H3K4me3_analysis is not a pre-defined dataset so can not be loaded. What are you trying to do in the fourth-from-last line of code? data(H3K4me3_analysis) -R ...
written 15 days ago by Rory Stark1.7k

Latest awards to Rory Stark

Scholar 14 days ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 16 days ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Autobiographer 5 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 10 months ago, created an answer that has been accepted. For A: ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single
Scholar 10 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 10 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 10 months ago, created an answer that has been accepted. For A: DiffBind matrix of values
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Scholar 12 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 14 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 15 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: diffBind correlation plot
Scholar 16 months ago, created an answer that has been accepted. For A: diffBind correlation plot
Scholar 16 months ago, created an answer that has been accepted. For A: Work with GRanges objects in DiffBind
Scholar 16 months ago, created an answer that has been accepted. For A: Clarification about the functionality of dba.count and dba.analyze
Scholar 16 months ago, created an answer that has been accepted. For A: subset of samples from dba object in DiffBind
Scholar 19 months ago, created an answer that has been accepted. For A: problem with characters in chromosome names in DiffBind dba
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: diffBind correlation plot
Scholar 21 months ago, created an answer that has been accepted. For A: diffBind correlation plot
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: diffBind correlation plot
Scholar 22 months ago, created an answer that has been accepted. For A: problem with characters in chromosome names in DiffBind dba
Scholar 22 months ago, created an answer that has been accepted. For A: DiffBind dba.peakset() and consensus peaks
Scholar 22 months ago, created an answer that has been accepted. For A: problem with characters in chromosome names in DiffBind dba
Scholar 22 months ago, created an answer that has been accepted. For A: problem with characters in chromosome names in DiffBind dba

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